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Common read and variant filters #154

Merged
merged 3 commits into from
May 20, 2015
Merged

Common read and variant filters #154

merged 3 commits into from
May 20, 2015

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fnothaft
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Pulled in several common read/variant filters.

Read filters:

  • Filter reads that have low base quality scores (this is @tdanford's code; @tdanford are you OK with the commit message I wrote for you?)
  • Filter reads that are marked as duplicates.
  • Filter reads that are badly soft clipped.

Variant filters:

  • Cleaned up the low coverage genotype filter.
  • Filter out multiallelic sites.
  • Filter out sites with high probability of strand bias under Fisher Exact Test model.

@fnothaft fnothaft mentioned this pull request Apr 25, 2015
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tdanford and others added 3 commits May 20, 2015 11:40
@tdanford @fnothaft
Added base quality score based read filters.
77871d3
@fnothaft
Miscellaneous read filter cleanup. Refactored preprocessing stages th…
cddd208 
…at filter reads to have a consistent interface.

Using this interface, I added filters to eliminate reads with high levels of soft clipping, and reads that are marked as duplicates.
@fnothaft
Updates to depth filter. Genotypes are not discarded, rather the filt…
db05a94 
…er string is set.

Further, refactored depth filter to provide generalized attribute based genotype filter.
Using generalized filter, added strand bias filter and multiallelic site filter.
@AmplabJenkins
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Test PASSed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins/job/avocado-prb/98/
Test PASSed.

fnothaft added a commit that referenced this pull request May 20, 2015
@fnothaft
Merge pull request #154 from fnothaft/common-filters
4f66c6d 
Common read and variant filters
@fnothaft fnothaft merged commit 4f66c6d into bigdatagenomics:master May 20, 2015
@fnothaft fnothaft deleted the common-filters branch May 20, 2015 18:52
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3 participants
@fnothaft @AmplabJenkins @tdanford